1
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Makino T, Kanada R, Mori T, Miyazono KI, Komori Y, Yanagisawa H, Takada S, Tanokura M, Kikkawa M, Tomishige M. Tension-induced suppression of allosteric conformational changes coordinates kinesin-1 stepping. J Cell Biol 2025; 224:e202501253. [PMID: 40298806 PMCID: PMC12039583 DOI: 10.1083/jcb.202501253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2025] [Revised: 03/18/2025] [Accepted: 04/08/2025] [Indexed: 04/30/2025] Open
Abstract
Kinesin-1 walks along microtubules by alternating ATP hydrolysis and movement of its two motor domains ("head"). The detached head preferentially binds to the forward tubulin-binding site after ATP binds to the microtubule-bound head, but the mechanism preventing premature microtubule binding while the partner head awaits ATP remains unknown. Here, we examined the role of the neck linker, the segment connecting two heads, in this mechanism. Structural analyses of the nucleotide-free head revealed a bulge just ahead of the neck linker's base, creating an asymmetric constraint on its mobility. While the neck linker can stretch freely backward, it must navigate around this bulge to extend forward. We hypothesized that increased neck linker tension suppresses premature binding of the tethered head, which was supported by molecular dynamics simulations and single-molecule fluorescence assays. These findings demonstrate a tension-dependent allosteric mechanism that coordinates the movement of two heads, where neck linker tension modulates the allosteric conformational changes rather than directly affecting the nucleotide state.
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Affiliation(s)
- Tsukasa Makino
- Department of Applied Physics, The University of Tokyo, Tokyo, Japan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ryo Kanada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Teppei Mori
- Department of Applied Physics, The University of Tokyo, Tokyo, Japan
| | - Ken-ichi Miyazono
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuta Komori
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Haruaki Yanagisawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Michio Tomishige
- Department of Applied Physics, The University of Tokyo, Tokyo, Japan
- Department of Physical Sciences, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Japan
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2
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Zhu H, Terashi G, Farheen F, Nakamura T, Kihara D. AI-based quality assessment methods for protein structure models from cryo-EM. Curr Res Struct Biol 2025; 9:100164. [PMID: 39996138 PMCID: PMC11848767 DOI: 10.1016/j.crstbi.2025.100164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 01/23/2025] [Accepted: 01/29/2025] [Indexed: 02/26/2025] Open
Abstract
Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, with an increasing number of structures being determined by cryo-EM each year, many at higher resolutions. However, challenges remain in accurately interpreting cryo-EM maps. Inaccuracies can arise in regions of locally low resolution, where manual model building is more prone to errors. Validation scores for structure models have been developed to assess both the compatibility between map density and the structure, as well as the geometric and stereochemical properties of protein models. Recent advancements have introduced artificial intelligence (AI) into this field. These emerging AI-driven tools offer unique capabilities in the validation and refinement of cryo-EM-derived protein atomic models, potentially leading to more accurate protein structures and deeper insights into complex biological systems.
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Affiliation(s)
- Han Zhu
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Farhanaz Farheen
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Tsukasa Nakamura
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Structural Biology Research Center, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
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3
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Jia H, Guan Z, Ding J, Wang X, Tian D, Zhu Y, Zhang D, Liu Z, Ma L, Yin P. Structural insight into PIF6-mediated red light signal transduction of plant phytochrome B. Cell Discov 2025; 11:51. [PMID: 40404641 PMCID: PMC12098889 DOI: 10.1038/s41421-025-00802-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2024] [Accepted: 04/27/2025] [Indexed: 05/24/2025] Open
Abstract
The red/far-red light receptor phytochrome B (phyB) plays essential roles in regulating various plant development processes. PhyB exists in two distinct photoreversible forms: the inactive Pr form and the active Pfr form. phyB-Pfr binds phytochrome-interacting factors (PIFs) to transduce red light signals. Here, we determined the cryo-electron microscopy (cryo-EM) structures of the photoactivated phyB-Pfr‒PIF6 complex, the constitutively active mutant phyBY276H‒PIF6 complex, and the truncated phyBNY276H‒PIF6 complex. In these structures, two parallel phyB-Pfr molecules interact with one PIF6 molecule. Red light-triggered rotation of the PΦB D-ring leads to the conversion of hairpin loops into α helices and the "head-to-head" reassembly of phyB-Pfr N-terminal photosensory modules. The interaction between phyB-Pfr and PIF6 influences the dimerization and transcriptional activation activity of PIF6, and PIF6 stabilizes the N-terminal extension of phyB-Pfr and increases the Pr→Pfr photoconversion efficiency of phyB. Our findings reveal the molecular mechanisms underlying Pr→Pfr photoconversion and PIF6-mediated red light signal transduction of phyB.
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Affiliation(s)
- Hanli Jia
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Junya Ding
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Xiaoyu Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Dingfang Tian
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Yan Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Zhu Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Ling Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, Hubei, China.
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, Hubei, China.
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4
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Ghanbarpour A, Telusma B, Powell BM, Zhang JJ, Bolstad I, Vargas C, Keller S, Baker TA, Sauer RT, Davis JH. An asymmetric nautilus-like HflK/C assembly controls FtsH proteolysis of membrane proteins. EMBO J 2025; 44:2501-2513. [PMID: 40082723 PMCID: PMC12048511 DOI: 10.1038/s44318-025-00408-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 12/13/2024] [Accepted: 02/28/2025] [Indexed: 03/16/2025] Open
Abstract
The AAA protease FtsH associates with HflK/C subunits to form a megadalton-size complex that spans the inner membrane and extends into the periplasm of E. coli. How this bacterial complex and homologous assemblies in eukaryotic organelles recruit, extract, and degrade membrane-embedded substrates is unclear. Following the overproduction of protein components, recent cryo-EM structures showed symmetric HflK/C cages surrounding FtsH in a manner proposed to inhibit the degradation of membrane-embedded substrates. Here, we present structures of native protein complexes, in which HflK/C instead forms an asymmetric nautilus-shaped assembly with an entryway for membrane-embedded substrates to reach and be engaged by FtsH. Consistent with this nautilus-like structure, proteomic assays suggest that HflK/C enhances FtsH degradation of certain membrane-embedded substrates. Membrane curvature in our FtsH•HflK/C complexes is opposite that of surrounding membrane regions, a property that correlates with lipid scramblase activity and possibly with FtsH's function in the degradation of membrane-embedded proteins.
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Affiliation(s)
- Alireza Ghanbarpour
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02129, USA.
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, 63110, USA.
| | - Bertina Telusma
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02129, USA
| | - Barrett M Powell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02129, USA
| | - Jia Jia Zhang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02129, USA
| | - Isabella Bolstad
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02129, USA
| | - Carolyn Vargas
- Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, Graz, 8010, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Sandro Keller
- Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, Graz, 8010, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Tania A Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02129, USA
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02129, USA.
| | - Joseph H Davis
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02129, USA.
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, 02129, USA.
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5
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Tai MDS, Ochoa L, Flydal MI, Velasco-Carneros L, Muntaner J, Santiago C, Gamiz-Arco G, Moro F, Jung-Kc K, Gil-Cantero D, Marcilla M, Kallio JP, Muga A, Valpuesta JM, Cuéllar J, Martinez A. Structural recognition and stabilization of tyrosine hydroxylase by the J-domain protein DNAJC12. Nat Commun 2025; 16:2755. [PMID: 40113792 PMCID: PMC11926245 DOI: 10.1038/s41467-025-57733-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/28/2025] [Indexed: 03/22/2025] Open
Abstract
Pathogenic variants of the J-domain protein DNAJC12 cause parkinsonism, which is associated with a defective interaction of DNAJC12 with tyrosine hydroxylase (TH), the rate-limiting enzyme in dopamine biosynthesis. In this work, we characterize the formation of the TH:DNAJC12 complex, showing that DNAJC12 binding stabilizes both TH and the variant TH-p.R202H, associated with TH deficiency. This binding delays their time-dependent aggregation in an Hsp70-independent manner, while preserving TH activity and feedback regulatory inhibition by dopamine. DNAJC12 alone barely activates Hsc70 but synergistically stimulates Hsc70 ATPase activity when complexed with TH. Cryo-electron microscopy supported by crosslinking-mass spectroscopy reveals two DNAJC12 monomers bound per TH tetramer, each embracing one of the two regulatory domain dimers, leaving the active sites available for substrate, cofactor and inhibitory dopamine interaction. Our results also reveal the key role of the C-terminal region of DNAJC12 in TH binding, explaining the pathogenic mechanism of the DNAJC12 disease variant p.W175Ter.
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Affiliation(s)
- Mary Dayne S Tai
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Neuro-SysMed Center, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Lissette Ochoa
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Marte I Flydal
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Lorea Velasco-Carneros
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena, Leioa, Spain
| | | | - César Santiago
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Gloria Gamiz-Arco
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Neuro-SysMed Center, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Fernando Moro
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena, Leioa, Spain
| | - Kunwar Jung-Kc
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Neuro-SysMed Center, Department of Neurology, Haukeland University Hospital, Bergen, Norway
- K.G Jebsen Center for Translational Research in Parkinson's Disease, University of Bergen, Bergen, Norway
| | | | | | - Juha P Kallio
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Arturo Muga
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena, Leioa, Spain
| | - José María Valpuesta
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
- Unidad de Nanobiotecnología, CNB-CSIC-IMDEA Nanociencia Associated Unit, Madrid, Spain.
| | - Jorge Cuéllar
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- Neuro-SysMed Center, Department of Neurology, Haukeland University Hospital, Bergen, Norway.
- K.G Jebsen Center for Translational Research in Parkinson's Disease, University of Bergen, Bergen, Norway.
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6
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Muenks A, Farrell DP, Zhou G, DiMaio F. Automated identification of small molecules in cryo-electron microscopy data with density- and energy-guided evaluation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.20.623795. [PMID: 39605546 PMCID: PMC11601544 DOI: 10.1101/2024.11.20.623795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Methodological improvements in cryo-electron microscopy (cryoEM) have made it a useful tool in ligand-bound structure determination for biology and drug design. However, determining the conformation and identity of bound ligands is still challenging at the resolutions typical for cryoEM. Automated methods can aid in ligand conformational modeling, but current ligand identification tools - developed for X-ray crystallography data - perform poorly at resolutions common for cryoEM. Here, we present EMERALD-ID, a method capable of docking and evaluating small molecule conformations for ligand identification. EMERALD-ID identifies 43% of common ligands exactly and identifies closely related ligands in 66% of cases. We then use this tool to discover possible ligand identification errors, as well as previously unidentified ligands. Furthermore, we show EMERALD-ID is capable of identifying ligands from custom ligand libraries of various small molecule types, including human metabolites and drug fragments. Our method provides a valuable addition to cryoEM modeling tools to improve small molecule model accuracy and quality.
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Affiliation(s)
- Andrew Muenks
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Daniel P. Farrell
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Guangfeng Zhou
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Lead contact
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7
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Gil-Cantero D, Mata CP, Valiente L, Rodríguez-Huete A, Valbuena A, Twarock R, Stockley PG, Mateu MG, Castón JR. Cryo-EM of human rhinovirus reveals capsid-RNA duplex interactions that provide insights into virus assembly and genome uncoating. Commun Biol 2024; 7:1501. [PMID: 39537894 PMCID: PMC11561273 DOI: 10.1038/s42003-024-07213-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 11/05/2024] [Indexed: 11/16/2024] Open
Abstract
The cryo-EM structure of the human rhinovirus B14 determined in this study reveals 13-bp RNA duplexes symmetrically bound to regions around each of the 30 two-fold axes in the icosahedral viral capsid. The RNA duplexes (~12% of the ssRNA genome) define a quasi-dodecahedral cage that line a substantial part of the capsid interior surface. The RNA duplexes establish a complex network of non-covalent interactions with pockets in the capsid inner wall, including coulombic interactions with a cluster of basic amino acid residues that surround each RNA duplex. A direct comparison was made between the cryo-EM structure of RNA-filled virions and that of RNA-free (empty) capsids that resulted from genome release from a small fraction of viruses. The comparison reveals that some specific residues involved in capsid-duplex RNA interactions in the virion undergo remarkable conformational rearrangements upon RNA release from the capsid. RNA release is also associated with the asynchronous opening of channels at the 30 two-fold axes. The results provide further insights into the molecular mechanisms leading to assembly of rhinovirus particles and their genome uncoating during infection. They may also contribute to development of novel antiviral strategies aimed at interfering with viral capsid-genome interactions during the infectious cycle.
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Affiliation(s)
- David Gil-Cantero
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Carlos P Mata
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Biocomputing Unit, Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Luis Valiente
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Alicia Rodríguez-Huete
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Reidun Twarock
- Department of Mathematics and Department of Biology, University of York, York, UK
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.
| | - José R Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain.
- Nanobiotechnology Associated Unit CNB-CSIC-IMDEA, Campus Cantoblanco, Madrid, Spain.
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8
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Ghanbarpour A, Sauer RT, Davis JH. A proteolytic AAA+ machine poised to unfold protein substrates. Nat Commun 2024; 15:9681. [PMID: 39516482 PMCID: PMC11549327 DOI: 10.1038/s41467-024-53681-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 10/18/2024] [Indexed: 11/16/2024] Open
Abstract
AAA+ proteolytic machines unfold proteins before degrading them. Here, we present cryoEM structures of ClpXP-substrate complexes that reveal a postulated but heretofore unseen intermediate in substrate unfolding/degradation. A ClpX hexamer draws natively folded substrates tightly against its axial channel via interactions with a fused C-terminal degron tail and ClpX-RKH loops that flexibly conform to the globular substrate. The specific ClpX-substrate contacts observed vary depending on the substrate degron and affinity tags, helping to explain ClpXP's ability to unfold/degrade a wide array of different cellular substrates. Some ClpX contacts with native substrates are enabled by upward movement of the seam subunit in the AAA+ spiral, a motion coupled to a rearrangement of contacts between the ClpX unfoldase and ClpP peptidase. Our structures additionally highlight ClpX's ability to translocate a diverse array of substrate topologies, including the co-translocation of two polypeptide chains.
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Affiliation(s)
- Alireza Ghanbarpour
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St Louis, 63130, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, USA
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, USA.
| | - Joseph H Davis
- Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, USA.
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9
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Mahalingan KK, Grotjahn DA, Li Y, Lander GC, Zehr EA, Roll-Mecak A. Structural basis for α-tubulin-specific and modification state-dependent glutamylation. Nat Chem Biol 2024; 20:1493-1504. [PMID: 38658656 PMCID: PMC11529724 DOI: 10.1038/s41589-024-01599-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 03/06/2024] [Indexed: 04/26/2024]
Abstract
Microtubules have spatiotemporally complex posttranslational modification patterns. Tubulin tyrosine ligase-like (TTLL) enzymes introduce the most prevalent modifications on α-tubulin and β-tubulin. How TTLLs specialize for specific substrate recognition and ultimately modification-pattern generation is largely unknown. TTLL6, a glutamylase implicated in ciliopathies, preferentially modifies tubulin α-tails in microtubules. Cryo-electron microscopy, kinetic analysis and single-molecule biochemistry reveal an unprecedented quadrivalent recognition that ensures simultaneous readout of microtubule geometry and posttranslational modification status. By binding to a β-tubulin subunit, TTLL6 modifies the α-tail of the longitudinally adjacent tubulin dimer. Spanning two tubulin dimers along and across protofilaments (PFs) ensures fidelity of recognition of both the α-tail and the microtubule. Moreover, TTLL6 reads out and is stimulated by glutamylation of the β-tail of the laterally adjacent tubulin dimer, mediating crosstalk between α-tail and β-tail. This positive feedback loop can generate localized microtubule glutamylation patterns. Our work uncovers general principles that generate tubulin chemical and topographic complexity.
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Affiliation(s)
- Kishore K Mahalingan
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Danielle A Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute La Jolla, La Jolla, CA, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute La Jolla, La Jolla, CA, USA
| | - Elena A Zehr
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
- Biochemistry & Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA.
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10
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Ghanbarpour A, Telusma B, Powell BM, Zhang JJ, Bolstad I, Vargas C, Keller S, Baker T, Sauer RT, Davis JH. An asymmetric nautilus-like HflK/C assembly controls FtsH proteolysis of membrane proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.604662. [PMID: 39149393 PMCID: PMC11326279 DOI: 10.1101/2024.08.09.604662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
FtsH, a AAA protease, associates with HflK/C subunits to form a megadalton complex that spans the inner membrane and extends into the periplasm of E. coli. How this complex and homologous assemblies in eukaryotic organelles recruit, extract, and degrade membrane-embedded substrates is unclear. Following overproduction of protein components, recent cryo-EM structures reveal symmetric HflK/C cages surrounding FtsH in a manner proposed to inhibit degradation of membrane-embedded substrates. Here, we present structures of native complexes in which HflK/C instead forms an asymmetric nautilus-like assembly with an entryway for membrane-embedded substrates to reach and be engaged by FtsH. Consistent with this nautilus-like structure, proteomic assays suggest that HflK/C enhances FtsH degradation of certain membrane-embedded substrates. The membrane curvature in our FtsH•HflK/C complexes is opposite that of surrounding membrane regions, a property that correlates with lipid-scramblase activity and possibly with FtsH's function in the degradation of membrane-embedded proteins.
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Affiliation(s)
- Alireza Ghanbarpour
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Bertina Telusma
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Barrett M Powell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jia Jia Zhang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Isabella Bolstad
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Carolyn Vargas
- Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz Austria
| | - Sandro Keller
- Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz Austria
| | - Tania Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Joseph H Davis
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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11
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Li A, You T, Pang X, Wang Y, Tian L, Li X, Liu Z. Structural basis for an early stage of the photosystem II repair cycle in Chlamydomonas reinhardtii. Nat Commun 2024; 15:5211. [PMID: 38890314 PMCID: PMC11189392 DOI: 10.1038/s41467-024-49532-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
Photosystem II (PSII) catalyzes water oxidation and plastoquinone reduction by utilizing light energy. It is highly susceptible to photodamage under high-light conditions and the damaged PSII needs to be restored through a process known as the PSII repair cycle. The detailed molecular mechanism underlying the PSII repair process remains mostly elusive. Here, we report biochemical and structural features of a PSII-repair intermediate complex, likely arrested at an early stage of the PSII repair process in the green alga Chlamydomonas reinhardtii. The complex contains three protein factors associated with a damaged PSII core, namely Thylakoid Enriched Factor 14 (TEF14), Photosystem II Repair Factor 1 (PRF1), and Photosystem II Repair Factor 2 (PRF2). TEF14, PRF1 and PRF2 may facilitate the release of the manganese-stabilizing protein PsbO, disassembly of peripheral light-harvesting complexes from PSII and blockage of the QB site, respectively. Moreover, an α-tocopherol quinone molecule is located adjacent to the heme group of cytochrome b559, potentially fulfilling a photoprotective role by preventing the generation of reactive oxygen species.
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Affiliation(s)
- Anjie Li
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Tingting You
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, China
| | - Xiaojie Pang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yidi Wang
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Lijin Tian
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaobo Li
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, 310024, China.
| | - Zhenfeng Liu
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China.
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12
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Grba DN, Wright JJ, Yin Z, Fisher W, Hirst J. Molecular mechanism of the ischemia-induced regulatory switch in mammalian complex I. Science 2024; 384:1247-1253. [PMID: 38870289 DOI: 10.1126/science.ado2075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/01/2024] [Indexed: 06/15/2024]
Abstract
Respiratory complex I is an efficient driver for oxidative phosphorylation in mammalian mitochondria, but its uncontrolled catalysis under challenging conditions leads to oxidative stress and cellular damage. Ischemic conditions switch complex I from rapid, reversible catalysis into a dormant state that protects upon reoxygenation, but the molecular basis for the switch is unknown. We combined precise biochemical definition of complex I catalysis with high-resolution cryo-electron microscopy structures in the phospholipid bilayer of coupled vesicles to reveal the mechanism of the transition into the dormant state, modulated by membrane interactions. By implementing a versatile membrane system to unite structure and function, attributing catalytic and regulatory properties to specific structural states, we define how a conformational switch in complex I controls its physiological roles.
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Affiliation(s)
| | | | | | | | - Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
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13
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Jojoa-Cruz S, Dubin AE, Lee WH, Ward AB. Structure-guided mutagenesis of OSCAs reveals differential activation to mechanical stimuli. eLife 2024; 12:RP93147. [PMID: 38592763 PMCID: PMC11003742 DOI: 10.7554/elife.93147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024] Open
Abstract
The dimeric two-pore OSCA/TMEM63 family has recently been identified as mechanically activated ion channels. Previously, based on the unique features of the structure of OSCA1.2, we postulated the potential involvement of several structural elements in sensing membrane tension (Jojoa-Cruz et al., 2018). Interestingly, while OSCA1, 2, and 3 clades are activated by membrane stretch in cell-attached patches (i.e. they are stretch-activated channels), they differ in their ability to transduce membrane deformation induced by a blunt probe (poking). Here, in an effort to understand the domains contributing to mechanical signal transduction, we used cryo-electron microscopy to solve the structure of Arabidopsis thaliana (At) OSCA3.1, which, unlike AtOSCA1.2, only produced stretch- but not poke-activated currents in our initial characterization (Murthy et al., 2018). Mutagenesis and electrophysiological assessment of conserved and divergent putative mechanosensitive features of OSCA1.2 reveal a selective disruption of the macroscopic currents elicited by poking without considerable effects on stretch-activated currents (SAC). Our results support the involvement of the amphipathic helix and lipid-interacting residues in the membrane fenestration in the response to poking. Our findings position these two structural elements as potential sources of functional diversity within the family.
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Affiliation(s)
- Sebastian Jojoa-Cruz
- Department of Integrative Structural and Computational Biology, Scripps ResearchLa JollaUnited States
| | - Adrienne E Dubin
- Department of Integrative Structural and Computational Biology, Scripps ResearchLa JollaUnited States
- Department of Neuroscience, Scripps ResearchLa JollaUnited States
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, Scripps ResearchLa JollaUnited States
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, Scripps ResearchLa JollaUnited States
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14
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Sanchez-Garcia R, Gaullier G, Cuadra-Troncoso JM, Vargas J. Cryo-EM Map Anisotropy Can Be Attenuated by Map Post-Processing and a New Method for Its Estimation. Int J Mol Sci 2024; 25:3959. [PMID: 38612769 PMCID: PMC11012471 DOI: 10.3390/ijms25073959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
One of the most important challenges in cryogenic electron microscopy (cryo-EM) is the substantial number of samples that exhibit preferred orientations, which leads to an uneven coverage of the projection sphere. As a result, the overall quality of the reconstructed maps can be severely affected, as manifested by the presence of anisotropy in the map resolution. Several methods have been proposed to measure the directional resolution of maps in tandem with experimental protocols to address the problem of preferential orientations in cryo-EM. Following these works, in this manuscript we identified one potential limitation that may affect most of the existing methods and we proposed an alternative approach to evaluate the presence of preferential orientations in cryo-EM reconstructions. In addition, we also showed that some of the most recently proposed cryo-EM map post-processing algorithms can attenuate map anisotropy, thus offering alternative visualization opportunities for cases affected by moderate levels of preferential orientations.
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Affiliation(s)
- Ruben Sanchez-Garcia
- Department of Statistics, University of Oxford, 24–29 St Giles’, Oxford OX1 3LB, UK
| | - Guillaume Gaullier
- Department of Chemistry—Ångström, Uppsala University, Box 523, SE 751 20 Uppsala, Sweden;
| | - Jose Manuel Cuadra-Troncoso
- Departamento de Inteligencia Artificial, Universidad Nacional de Educación a Distancia, C. Juan del Rosal 16, 28040 Madrid, Spain;
| | - Javier Vargas
- Departamento de Óptica, Universidad Complutense de Madrid, Plaza de Ciencias 1, 28040 Madrid, Spain
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15
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Liu G, Niu T, Qiu M, Zhu Y, Sun F, Yang G. DeepETPicker: Fast and accurate 3D particle picking for cryo-electron tomography using weakly supervised deep learning. Nat Commun 2024; 15:2090. [PMID: 38453943 PMCID: PMC11258139 DOI: 10.1038/s41467-024-46041-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/12/2024] [Indexed: 03/09/2024] Open
Abstract
To solve three-dimensional structures of biological macromolecules in situ, large numbers of particles often need to be picked from cryo-electron tomograms. However, adoption of automated particle-picking methods remains limited because of their technical limitations. To overcome the limitations, we develop DeepETPicker, a deep learning model for fast and accurate picking of particles from cryo-electron tomograms. Training of DeepETPicker requires only weak supervision with low numbers of simplified labels, reducing the burden of manual annotation. The simplified labels combined with the customized and lightweight model architecture of DeepETPicker and accelerated pooling enable substantial performance improvement. When tested on simulated and real tomograms, DeepETPicker outperforms the competing state-of-the-art methods by achieving the highest overall accuracy and speed, which translate into higher authenticity and coordinates accuracy of picked particles and higher resolutions of final reconstruction maps. DeepETPicker is provided in open source with a user-friendly interface to support cryo-electron tomography in situ.
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Affiliation(s)
- Guole Liu
- State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
- National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tongxin Niu
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mengxuan Qiu
- State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
- National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fei Sun
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, 510005, China.
| | - Ge Yang
- State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China.
- National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China.
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.
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16
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Sievers K, Neumann P, Sušac L, Da Vela S, Graewert M, Trowitzsch S, Svergun D, Tampé R, Ficner R. Structural and functional insights into tRNA recognition by human tRNA guanine transglycosylase. Structure 2024; 32:316-327.e5. [PMID: 38181786 DOI: 10.1016/j.str.2023.12.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/06/2023] [Accepted: 12/08/2023] [Indexed: 01/07/2024]
Abstract
Eukaryotic tRNA guanine transglycosylase (TGT) is an RNA-modifying enzyme which catalyzes the base exchange of the genetically encoded guanine 34 of tRNAsAsp,Asn,His,Tyr for queuine, a hypermodified 7-deazaguanine derivative. Eukaryotic TGT is a heterodimer comprised of a catalytic and a non-catalytic subunit. While binding of the tRNA anticodon loop to the active site is structurally well understood, the contribution of the non-catalytic subunit to tRNA binding remained enigmatic, as no complex structure with a complete tRNA was available. Here, we report a cryo-EM structure of eukaryotic TGT in complex with a complete tRNA, revealing the crucial role of the non-catalytic subunit in tRNA binding. We decipher the functional significance of these additional tRNA-binding sites, analyze solution state conformation, flexibility, and disorder of apo TGT, and examine conformational transitions upon tRNA binding.
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Affiliation(s)
- Katharina Sievers
- Department of Molecular Structural Biology, GZMB, University of Göttingen, 37077 Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, GZMB, University of Göttingen, 37077 Göttingen, Germany
| | - Lukas Sušac
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Stefano Da Vela
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, 22607 Hamburg, Germany
| | - Melissa Graewert
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, 22607 Hamburg, Germany
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, 22607 Hamburg, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, GZMB, University of Göttingen, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany.
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17
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Jojoa-Cruz S, Dubin AE, Lee WH, Ward A. Structure-guided mutagenesis of OSCAs reveals differential activation to mechanical stimuli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.03.560740. [PMID: 37873218 PMCID: PMC10592937 DOI: 10.1101/2023.10.03.560740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The dimeric two-pore OSCA/TMEM63 family has recently been identified as mechanically activated ion channels. Previously, based on the unique features of the structure of OSCA1.2, we postulated the potential involvement of several structural elements in sensing membrane tension1. Interestingly, while OSCA1, 2, and 3 clades are activated by membrane stretch in cell-attached patches (i.e., they are stretch-activated channels), they differ in their ability to transduce membrane deformation induced by a blunt probe (poking). In an effort to understand the domains contributing to mechanical signal transduction, we used cryo-electron microscopy to solve the structure of Arabidopsis thaliana (At) OSCA3.1, which, unlike AtOSCA1.2, only produced stretch- but not poke-activated currents in our initial characterization2. Mutagenesis and electrophysiological assessment of conserved and divergent putative mechanosensitive features of OSCA1.2 reveal a selective disruption of the macroscopic currents elicited by poking without considerable effects on stretch-activated currents (SAC). Our results support the involvement of the amphipathic helix and lipid-interacting residues in the membrane fenestration in the response to poking. Our findings position these two structural elements as potential sources of functional diversity within the family.
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Affiliation(s)
- Sebastian Jojoa-Cruz
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California 92037, USA
| | - Adrienne E. Dubin
- Department of Neuroscience, Scripps Research, La Jolla, California 92037, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California 92037, USA
| | - Andrew Ward
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California 92037, USA
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18
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Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S. Community recommendations on cryoEM data archiving and validation. IUCRJ 2024; 11:140-151. [PMID: 38358351 PMCID: PMC10916293 DOI: 10.1107/s2052252524001246] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.
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Affiliation(s)
| | - Paul D. Adams
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California, Berkeley, CA, USA
| | | | | | | | | | | | - Maya Topf
- Birkbeck, University of London, London, United Kingdom
| | | | | | | | | | | | | | | | - Sai J. Ganesan
- University of California at San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Ryan Pye
- EMBL-EBI, Cambridge, United Kingdom
| | | | | | | | | | | | | | | | | | - Zhe Wang
- EMBL-EBI, Cambridge, United Kingdom
| | | | | | - Martyn D. Winn
- Science and Technology Facilities Council, Research Complex at Harwell, Oxon, United Kingdom
| | - Jasmine Y. Young
- RCSB Protein Data Bank, The State University of New Jersey, NJ, USA
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19
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Jojoa-Cruz S, Burendei B, Lee WH, Ward AB. Structure of mechanically activated ion channel OSCA2.3 reveals mobile elements in the transmembrane domain. Structure 2024; 32:157-167.e5. [PMID: 38103547 PMCID: PMC10872982 DOI: 10.1016/j.str.2023.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/29/2023] [Accepted: 11/21/2023] [Indexed: 12/19/2023]
Abstract
Members of the OSCA/TMEM63 family are mechanically activated ion channels and structures of some OSCA members have revealed the architecture of these channels and structural features that are potentially involved in mechanosensation. However, these structures are all in a similar state and information about the motion of different elements of the structure is limited, preventing a deeper understanding of how these channels work. Here, we used cryoelectron microscopy to determine high-resolution structures of Arabidopsis thaliana OSCA1.2 and OSCA2.3 in peptidiscs. The structure of OSCA1.2 matches previous structures of the same protein in different environments. Yet, in OSCA2.3, the TM6a-TM7 linker adopts a different conformation that constricts the pore on its cytoplasmic side. Furthermore, coevolutionary sequence analysis uncovered a conserved interaction between the TM6a-TM7 linker and the beam-like domain (BLD). Our results reveal conformational heterogeneity and differences in conserved interactions between the TMD and BLD among members of the OSCA family.
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Affiliation(s)
- Sebastian Jojoa-Cruz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Batuujin Burendei
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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20
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Ghanbarpour A, Sauer RT, Davis JH. A proteolytic AAA+ machine poised to unfold a protein substrate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571662. [PMID: 38168193 PMCID: PMC10760120 DOI: 10.1101/2023.12.14.571662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
AAA+ proteolytic machines unfold proteins prior to degradation. Cryo-EM of a ClpXP-substrate complex reveals a postulated but heretofore unseen intermediate in substrate unfolding/degradation. The natively folded substrate is drawn tightly against the ClpX channel by interactions between axial pore loops and the substrate degron tail, and by contacts with the native substrate that are, in part, enabled by movement of one ClpX subunit out of the typically observed hexameric spiral.
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Affiliation(s)
- Alireza Ghanbarpour
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Joseph H Davis
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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21
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Fernandez-Gimenez E, Carazo JM, Sorzano COS. Local defocus estimation in single particle analysis in cryo-electron microscopy. J Struct Biol 2023; 215:108030. [PMID: 37758154 DOI: 10.1016/j.jsb.2023.108030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/30/2023] [Accepted: 09/21/2023] [Indexed: 10/02/2023]
Abstract
Single Particle analysis (SPA) aims to determine the three-dimensional structure of proteins and macromolecular complexes. The current state of the art has allowed us to achieve near-atomic and even atomic resolutions. To obtain high-resolution structures, a set of well-defined image processing steps is required. A critical one is the estimation of the Contrast Transfer Function (CTF), which considers the sample defocus and aberrations of the microscope. Defocus is usually globally estimated; in this case, it is the same for all the particles in each micrograph. But proteins are ice-embedded at different heights, suggesting that defocus should be measured in a local (per particle) manner. There are four state-of-the-art programs to estimate local defocus (Gctf, Relion, CryoSPARC, and Xmipp). In this work, we have compared the results of these software packages to check whether the resolution improves. We have used the Scipion framework and developed a specific program to analyze local defocus. The results produced by different programs do not show a clear consensus using the current test datasets in this study.
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Affiliation(s)
- E Fernandez-Gimenez
- Centro Nac. Biotecnologia (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain; Univ. Autonoma de Madrid, 28049 Cantoblanco, Madrid, Spain
| | - J M Carazo
- Centro Nac. Biotecnologia (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - C O S Sorzano
- Centro Nac. Biotecnologia (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain.
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22
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Semchonok DA, Kyrilis FL, Hamdi F, Kastritis PL. Cryo-EM of a heterogeneous biochemical fraction elucidates multiple protein complexes from a multicellular thermophilic eukaryote. J Struct Biol X 2023; 8:100094. [PMID: 37638207 PMCID: PMC10451023 DOI: 10.1016/j.yjsbx.2023.100094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/29/2023] Open
Abstract
Biomolecular complexes and their interactions govern cellular structure and function. Understanding their architecture is a prerequisite for dissecting the cell's inner workings, but their higher-order assembly is often transient and challenging for structural analysis. Here, we performed cryo-EM on a single, highly heterogeneous biochemical fraction derived from Chaetomium thermophilum cell extracts to visualize the biomolecular content of the multicellular eukaryote. After cryo-EM single-particle image processing, results showed that a simultaneous three-dimensional structural characterization of multiple chemically diverse biomacromolecules is feasible. Namely, the thermophilic, eukaryotic complexes of (a) ATP citrate-lyase, (b) Hsp90, (c) 20S proteasome, (d) Hsp60 and (e) UDP-glucose pyrophosphorylase were characterized. In total, all five complexes have been structurally dissected in a thermophilic eukaryote in a total imaged sample area of 190.64 μm2, and two, in particular, 20S proteasome and Hsp60, exhibit side-chain resolution features. The C. thermophilum Hsp60 near-atomic model was resolved at 3.46 Å (FSC = 0.143) and shows a hinge-like conformational change of its equatorial domain, highly similar to the one previously shown for its bacterial orthologue, GroEL. This work demonstrates that cryo-EM of cell extracts will greatly accelerate the structural analysis of cellular complexes and provide unprecedented opportunities to annotate architectures of biomolecules in a holistic approach.
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Affiliation(s)
- Dmitry A. Semchonok
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Fotis L. Kyrilis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Farzad Hamdi
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Panagiotis L. Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
- Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, Halle/Saale, Germany
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23
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Fernández-Giménez E, Martínez MM, Marabini R, Strelak D, Sánchez-García R, Carazo JM, Sorzano COS. A new algorithm for particle weighted subtraction to decrease signals from unwanted components in single particle analysis. J Struct Biol 2023; 215:108024. [PMID: 37704013 DOI: 10.1016/j.jsb.2023.108024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/22/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023]
Abstract
Single particle analysis (SPA) in cryo-electron microscopy (cryo-EM) is highly used to obtain the near-atomic structure of biological macromolecules. The current methods allow users to produce high-resolution maps from many samples. However, there are still challenging cases that require extra processing to obtain high resolution. This is the case when the macromolecule of the sample is composed of different components and we want to focus just on one of them. For example, if the macromolecule is composed of several flexible subunits and we are interested in a specific one, if it is embedded in a viral capsid environment, or if it has additional components to stabilize it, such as nanodiscs. The signal from these components, which in principle we are not interested in, can be removed from the particles using a projection subtraction method. Currently, there are two projection subtraction methods used in practice and both have some limitations. In fact, after evaluating their results, we consider that the problem is still open to new solutions, as they do not fully remove the signal of the components that are not of interest. Our aim is to develop a new and more precise projection subtraction method, improving the performance of state-of-the-art methods. We tested our algorithm with data from public databases and an in-house data set. In this work, we show that the performance of our algorithm improves the results obtained by others, including the localization of small ligands, such as drugs, whose binding location is unknown a priori.
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Affiliation(s)
- E Fernández-Giménez
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain; Univ. Autonoma de Madrid, 28049 Cantoblanco, Madrid, Spain
| | - M M Martínez
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - R Marabini
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain; Univ. Autonoma de Madrid, 28049 Cantoblanco, Madrid, Spain
| | - D Strelak
- Institute of Computer Science, Masaryk University, Botanická 68a, 60200 Brno, Czech Republic
| | - R Sánchez-García
- Department of Statistics, University of Oxford, 24-29 St Giles', Oxford OX1 3LB, United Kingdom; Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, UK
| | - J M Carazo
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - C O S Sorzano
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain.
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24
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Ghanbarpour A, Cohen SE, Fei X, Kinman LF, Bell TA, Zhang JJ, Baker TA, Davis JH, Sauer RT. A closed translocation channel in the substrate-free AAA+ ClpXP protease diminishes rogue degradation. Nat Commun 2023; 14:7281. [PMID: 37949857 PMCID: PMC10638403 DOI: 10.1038/s41467-023-43145-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/01/2023] [Indexed: 11/12/2023] Open
Abstract
AAA+ proteases degrade intracellular proteins in a highly specific manner. E. coli ClpXP, for example, relies on a C-terminal ssrA tag or other terminal degron sequences to recognize proteins, which are then unfolded by ClpX and subsequently translocated through its axial channel and into the degradation chamber of ClpP for proteolysis. Prior cryo-EM structures reveal that the ssrA tag initially binds to a ClpX conformation in which the axial channel is closed by a pore-2 loop. Here, we show that substrate-free ClpXP has a nearly identical closed-channel conformation. We destabilize this closed-channel conformation by deleting residues from the ClpX pore-2 loop. Strikingly, open-channel ClpXP variants degrade non-native proteins lacking degrons faster than the parental enzymes in vitro but degraded GFP-ssrA more slowly. When expressed in E. coli, these open channel variants behave similarly to the wild-type enzyme in assays of filamentation and phage-Mu plating but resulted in reduced growth phenotypes at elevated temperatures or when cells were exposed to sub-lethal antibiotic concentrations. Thus, channel closure is an important determinant of ClpXP degradation specificity.
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Affiliation(s)
- Alireza Ghanbarpour
- Department of Biology Massachusetts Institute of Technology Cambridge, Cambridge, MA, 02139, USA
| | - Steven E Cohen
- Department of Biology Massachusetts Institute of Technology Cambridge, Cambridge, MA, 02139, USA
| | - Xue Fei
- Department of Biology Massachusetts Institute of Technology Cambridge, Cambridge, MA, 02139, USA
| | - Laurel F Kinman
- Department of Biology Massachusetts Institute of Technology Cambridge, Cambridge, MA, 02139, USA
| | - Tristan A Bell
- Department of Biology Massachusetts Institute of Technology Cambridge, Cambridge, MA, 02139, USA
| | - Jia Jia Zhang
- Department of Biology Massachusetts Institute of Technology Cambridge, Cambridge, MA, 02139, USA
| | - Tania A Baker
- Department of Biology Massachusetts Institute of Technology Cambridge, Cambridge, MA, 02139, USA
| | - Joseph H Davis
- Department of Biology Massachusetts Institute of Technology Cambridge, Cambridge, MA, 02139, USA.
| | - Robert T Sauer
- Department of Biology Massachusetts Institute of Technology Cambridge, Cambridge, MA, 02139, USA.
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25
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Abbasi Yeganeh F, Rastegarpouyani H, Li J, Taylor KA. Structure of the Drosophila melanogaster Flight Muscle Myosin Filament at 4.7 Å Resolution Reveals New Details of Non-Myosin Proteins. Int J Mol Sci 2023; 24:14936. [PMID: 37834384 PMCID: PMC10573858 DOI: 10.3390/ijms241914936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 09/29/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023] Open
Abstract
Striated muscle thick filaments are composed of myosin II and several non-myosin proteins which define the filament length and modify its function. Myosin II has a globular N-terminal motor domain comprising its catalytic and actin-binding activities and a long α-helical, coiled tail that forms the dense filament backbone. Myosin alone polymerizes into filaments of irregular length, but striated muscle thick filaments have defined lengths that, with thin filaments, define the sarcomere structure. The motor domain structure and function are well understood, but the myosin filament backbone is not. Here we report on the structure of the flight muscle thick filaments from Drosophila melanogaster at 4.7 Å resolution, which eliminates previous ambiguities in non-myosin densities. The full proximal S2 region is resolved, as are the connecting densities between the Ig domains of stretchin-klp. The proteins, flightin, and myofilin are resolved in sufficient detail to build an atomic model based on an AlphaFold prediction. Our results suggest a method by which flightin and myofilin cooperate to define the structure of the thick filament and explains a key myosin mutation that affects flightin incorporation. Drosophila is a genetic model organism for which our results can define strategies for functional testing.
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Affiliation(s)
- Fatemeh Abbasi Yeganeh
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA; (F.A.Y.); (H.R.); (J.L.)
| | - Hosna Rastegarpouyani
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA; (F.A.Y.); (H.R.); (J.L.)
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4380, USA
| | - Jiawei Li
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA; (F.A.Y.); (H.R.); (J.L.)
| | - Kenneth A. Taylor
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA; (F.A.Y.); (H.R.); (J.L.)
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26
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Wright KM, DiNapoli SR, Miller MS, Aitana Azurmendi P, Zhao X, Yu Z, Chakrabarti M, Shi W, Douglass J, Hwang MS, Hsiue EHC, Mog BJ, Pearlman AH, Paul S, Konig MF, Pardoll DM, Bettegowda C, Papadopoulos N, Kinzler KW, Vogelstein B, Zhou S, Gabelli SB. Hydrophobic interactions dominate the recognition of a KRAS G12V neoantigen. Nat Commun 2023; 14:5063. [PMID: 37604828 PMCID: PMC10442379 DOI: 10.1038/s41467-023-40821-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 08/10/2023] [Indexed: 08/23/2023] Open
Abstract
Specificity remains a major challenge to current therapeutic strategies for cancer. Mutation associated neoantigens (MANAs) are products of genetic alterations, making them highly specific therapeutic targets. MANAs are HLA-presented (pHLA) peptides derived from intracellular mutant proteins that are otherwise inaccessible to antibody-based therapeutics. Here, we describe the cryo-EM structure of an antibody-MANA pHLA complex. Specifically, we determine a TCR mimic (TCRm) antibody bound to its MANA target, the KRASG12V peptide presented by HLA-A*03:01. Hydrophobic residues appear to account for the specificity of the mutant G12V residue. We also determine the structure of the wild-type G12 peptide bound to HLA-A*03:01, using X-ray crystallography. Based on these structures, we perform screens to validate the key residues required for peptide specificity. These experiments led us to a model for discrimination between the mutant and the wild-type peptides presented on HLA-A*03:01 based exclusively on hydrophobic interactions.
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Affiliation(s)
- Katharine M Wright
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA
- Discovery Chemistry, Protein and Structural Chemistry, Merck & Co, Inc, West Point, PA, 19846, USA
| | - Sarah R DiNapoli
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Michelle S Miller
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
| | - P Aitana Azurmendi
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA
| | - Xiaowei Zhao
- Janelia Research Campus, HHMI,19700 Helix Drive, Ashburn, VA, 20147, USA
| | - Zhiheng Yu
- Janelia Research Campus, HHMI,19700 Helix Drive, Ashburn, VA, 20147, USA
| | - Mayukh Chakrabarti
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - WuXian Shi
- Energy & Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY, 11973, USA
- Case Center for Synchrotron Biosciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Jacqueline Douglass
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Michael S Hwang
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Emily Han-Chung Hsiue
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Novartis Institutes for BioMedical Research, 250 Massachusetts Ave, Cambridge, MA, 02139, USA
| | - Brian J Mog
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Alexander H Pearlman
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Suman Paul
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Division of Hematologic Malignancies and Bone Marrow Transplantation, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Maximilian F Konig
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA
| | - Drew M Pardoll
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Chetan Bettegowda
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Nickolas Papadopoulos
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Kenneth W Kinzler
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Bert Vogelstein
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Shibin Zhou
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA.
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
| | - Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Discovery Chemistry, Protein and Structural Chemistry, Merck & Co, Inc, West Point, PA, 19846, USA.
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27
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Conesa P, Fonseca YC, Jiménez de la Morena J, Sharov G, de la Rosa-Trevín JM, Cuervo A, García Mena A, Rodríguez de Francisco B, del Hoyo D, Herreros D, Marchan D, Strelak D, Fernández-Giménez E, Ramírez-Aportela E, de Isidro-Gómez FP, Sánchez I, Krieger J, Vilas JL, del Cano L, Gragera M, Iceta M, Martínez M, Losana P, Melero R, Marabini R, Carazo JM, Sorzano COS. Scipion3: A workflow engine for cryo-electron microscopy image processing and structural biology. BIOLOGICAL IMAGING 2023; 3:e13. [PMID: 38510163 PMCID: PMC10951921 DOI: 10.1017/s2633903x23000132] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/29/2023] [Accepted: 06/15/2023] [Indexed: 03/22/2024]
Abstract
Image-processing pipelines require the design of complex workflows combining many different steps that bring the raw acquired data to a final result with biological meaning. In the image-processing domain of cryo-electron microscopy single-particle analysis (cryo-EM SPA), hundreds of steps must be performed to obtain the three-dimensional structure of a biological macromolecule by integrating data spread over thousands of micrographs containing millions of copies of allegedly the same macromolecule. The execution of such complicated workflows demands a specific tool to keep track of all these steps performed. Additionally, due to the extremely low signal-to-noise ratio (SNR), the estimation of any image parameter is heavily affected by noise resulting in a significant fraction of incorrect estimates. Although low SNR and processing millions of images by hundreds of sequential steps requiring substantial computational resources are specific to cryo-EM, these characteristics may be shared by other biological imaging domains. Here, we present Scipion, a Python generic open-source workflow engine specifically adapted for image processing. Its main characteristics are: (a) interoperability, (b) smart object model, (c) gluing operations, (d) comparison operations, (e) wide set of domain-specific operations, (f) execution in streaming, (g) smooth integration in high-performance computing environments, (h) execution with and without graphical capabilities, (i) flexible visualization, (j) user authentication and private access to private data, (k) scripting capabilities, (l) high performance, (m) traceability, (n) reproducibility, (o) self-reporting, (p) reusability, (q) extensibility, (r) software updates, and (s) non-restrictive software licensing.
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Affiliation(s)
- Pablo Conesa
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | | | | | - Grigory Sharov
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Ana Cuervo
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | | | | | | | - David Herreros
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Daniel Marchan
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - David Strelak
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
- Masaryk University, Brno, Czech Republic
| | | | | | | | - Irene Sánchez
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - James Krieger
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | | | - Laura del Cano
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Marcos Gragera
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Mikel Iceta
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Marta Martínez
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | | | - Roberto Melero
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Roberto Marabini
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
- Superior Polytechnic School, Autonomous University of Madrid, Madrid, Spain
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28
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Lunin VY, Lunina NL, Urzhumtsev AG. Local heterogeneity analysis of crystallographic and cryo-EM maps using shell-approximation. Curr Res Struct Biol 2023; 6:100102. [PMID: 37424695 PMCID: PMC10329102 DOI: 10.1016/j.crstbi.2023.100102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 07/11/2023] Open
Abstract
In X-ray crystallography and cryo-EM, experimental maps can be heterogeneous, showing different level of details in different regions. In this work we interpret heterogeneity in terms of two parameters, assigned individually for each atom, combining the conventional atomic displacement parameter with the resolution of the atomic image in the map. We propose a local real-space procedure to estimate the values of these heterogeneity parameters, assuming that a fragment of the density map and atomic positions are given. The procedure is based on an analytic representation of the atomic image, as a function of the inhomogeneity parameters and atomic coordinates. In this article, we report the results of the tests both with maps simulated and those derived from experimental data. For simulated maps containing regions with different resolutions, the method determines the local map resolution around the atomic centers and the values of the displacement parameter with reasonable accuracy. For experimental maps, obtained as a Fourier synthesis of a given global resolution, estimated values of the local resolution are close to the global one, and the values of the estimated displacement parameters are close to the respective values of the closest atoms in the refined model. Shown successful applications of the proposed method to experimental crystallographic and cryo-EM maps can be seen as a practical proof of method.
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Affiliation(s)
- Vladimir Y. Lunin
- Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 1, Professor Vitkevich St., Pushchino, 142290, Russia
| | - Natalia L. Lunina
- Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 1, Professor Vitkevich St., Pushchino, 142290, Russia
| | - Alexandre G. Urzhumtsev
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France
- Université de Lorraine, Faculté des Sciences et Technologies, BP 239, 54506, Vandoeuvre-les-Nancy, France
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29
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Shlosman I, Fivenson EM, Gilman MSA, Sisley TA, Walker S, Bernhardt TG, Kruse AC, Loparo JJ. Allosteric activation of cell wall synthesis during bacterial growth. Nat Commun 2023; 14:3439. [PMID: 37301887 PMCID: PMC10257715 DOI: 10.1038/s41467-023-39037-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
The peptidoglycan (PG) cell wall protects bacteria against osmotic lysis and determines cell shape, making this structure a key antibiotic target. Peptidoglycan is a polymer of glycan chains connected by peptide crosslinks, and its synthesis requires precise spatiotemporal coordination between glycan polymerization and crosslinking. However, the molecular mechanism by which these reactions are initiated and coupled is unclear. Here we use single-molecule FRET and cryo-EM to show that an essential PG synthase (RodA-PBP2) responsible for bacterial elongation undergoes dynamic exchange between closed and open states. Structural opening couples the activation of polymerization and crosslinking and is essential in vivo. Given the high conservation of this family of synthases, the opening motion that we uncovered likely represents a conserved regulatory mechanism that controls the activation of PG synthesis during other cellular processes, including cell division.
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Affiliation(s)
- Irina Shlosman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Elayne M Fivenson
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Morgan S A Gilman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Tyler A Sisley
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Suzanne Walker
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.
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30
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He J, Li T, Huang SY. Improvement of cryo-EM maps by simultaneous local and non-local deep learning. Nat Commun 2023; 14:3217. [PMID: 37270635 DOI: 10.1038/s41467-023-39031-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 05/25/2023] [Indexed: 06/05/2023] Open
Abstract
Cryo-EM has emerged as the most important technique for structure determination of macromolecular complexes. However, raw cryo-EM maps often exhibit loss of contrast at high resolution and heterogeneity over the entire map. As such, various post-processing methods have been proposed to improve cryo-EM maps. Nevertheless, it is still challenging to improve both the quality and interpretability of EM maps. Addressing the challenge, we present a three-dimensional Swin-Conv-UNet-based deep learning framework to improve cryo-EM maps, named EMReady, by not only implementing both local and non-local modeling modules in a multiscale UNet architecture but also simultaneously minimizing the local smooth L1 distance and maximizing the non-local structural similarity between processed experimental and simulated target maps in the loss function. EMReady was extensively evaluated on diverse test sets of 110 primary cryo-EM maps and 25 pairs of half-maps at 3.0-6.0 Å resolutions, and compared with five state-of-the-art map post-processing methods. It is shown that EMReady can not only robustly enhance the quality of cryo-EM maps in terms of map-model correlations, but also improve the interpretability of the maps in automatic de novo model building.
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Affiliation(s)
- Jiahua He
- School of Physics and Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Li
- School of Physics and Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, China
| | - Sheng-You Huang
- School of Physics and Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, China.
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31
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Matsumoto S, Ishida S, Terayama K, Okuno Y. Quantitative analysis of protein dynamics using a deep learning technique combined with experimental cryo-EM density data and MD simulations. Biophys Physicobiol 2023; 20:e200022. [PMID: 38496243 PMCID: PMC10941960 DOI: 10.2142/biophysico.bppb-v20.0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/12/2023] [Indexed: 03/19/2024] Open
Abstract
Protein functions associated with biological activity are precisely regulated by both tertiary structure and dynamic behavior. Thus, elucidating the high-resolution structures and quantitative information on in-solution dynamics is essential for understanding the molecular mechanisms. The main experimental approaches for determining tertiary structures include nuclear magnetic resonance (NMR), X-ray crystallography, and cryogenic electron microscopy (cryo-EM). Among these procedures, recent remarkable advances in the hardware and analytical techniques of cryo-EM have increasingly determined novel atomic structures of macromolecules, especially those with large molecular weights and complex assemblies. In addition to these experimental approaches, deep learning techniques, such as AlphaFold 2, accurately predict structures from amino acid sequences, accelerating structural biology research. Meanwhile, the quantitative analyses of the protein dynamics are conducted using experimental approaches, such as NMR and hydrogen-deuterium mass spectrometry, and computational approaches, such as molecular dynamics (MD) simulations. Although these procedures can quantitatively explore dynamic behavior at high resolution, the fundamental difficulties, such as signal crowding and high computational cost, greatly hinder their application to large and complex biological macromolecules. In recent years, machine learning techniques, especially deep learning techniques, have been actively applied to structural data to identify features that are difficult for humans to recognize from big data. Here, we review our approach to accurately estimate dynamic properties associated with local fluctuations from three-dimensional cryo-EM density data using a deep learning technique combined with MD simulations.
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Affiliation(s)
| | - Shoichi Ishida
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Kei Terayama
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Yasuhshi Okuno
- Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
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32
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Herreros D, Kiska J, Ramirez E, Filipovic J, Carazo JM, Sorzano COS. ZART: A novel multiresolution reconstruction algorithm with motion-blur correction for single particle analysis. J Mol Biol 2023; 435:168088. [PMID: 37030648 DOI: 10.1016/j.jmb.2023.168088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/31/2023] [Accepted: 04/01/2023] [Indexed: 04/10/2023]
Abstract
One of the main purposes of CryoEM Single Particle Analysis is to reconstruct the three-dimensional structure of a macromolecule thanks to the acquisition of many particle images representing different poses of the sample. By estimating the orientation of each projected particle, it is possible to recover the underlying 3D volume by multiple 3D reconstruction methods, usually working either in Fourier or in real space. However, the reconstruction from the projected images works under the assumption that all particles in the dataset correspond to the same conformation of the macromolecule. Although this requisite holds for some macromolecules, it is not true for flexible specimens, leading to motion-induced artefacts in the reconstructed CryoEM maps. In this work, we introduce a new Algebraic Reconstruction Technique called ZART, which is able to include continuous flexibility information during the reconstruction process to improve local resolution and reduce motion blurring. The conformational changes are modelled through Zernike3D polynomials. Our implementation allows for a multiresolution description of the macromolecule adapting itself to the local resolution of the reconstructed map. In addition, ZART has also proven to be a useful algorithm in cases where flexibility is not so dominant, as it improves the overall aspect of the reconstructed maps by improving their local and global resolution.
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Affiliation(s)
- D Herreros
- Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain.
| | - J Kiska
- Institute of Computer Science, Masaryk University, Botanická 68a, 60200 Brno, Czech Republic
| | - E Ramirez
- Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain
| | - J Filipovic
- Institute of Computer Science, Masaryk University, Botanická 68a, 60200 Brno, Czech Republic
| | - J M Carazo
- Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain.
| | - C O S Sorzano
- Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain.
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33
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Dai M, Dong Z, Xu K, Cliff Zhang Q. CryoRes: Local Resolution Estimation of Cryo-EM Density Maps by Deep Learning. J Mol Biol 2023; 435:168059. [PMID: 36967040 DOI: 10.1016/j.jmb.2023.168059] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 03/15/2023] [Accepted: 03/21/2023] [Indexed: 04/03/2023]
Abstract
Recent progress in cryo-EM research has ignited a revolution in biological macromolecule structure determination. Resolution is an essential parameter for quality assessment of a cryo-EM density map, and it is known that resolution varies in different regions of a map. Currently available methods for local resolution estimation require manual adjustment of parameters and in some cases necessitate acquisition or de novo generation of so-called "half maps". Here, we developed CryoRes, a deep-learning algorithm to estimate local resolution directly from a single final cryo-EM density map, specifically by learning resolution-aware patterns of density map voxels through supervised training on a large dataset comprising 1,174 experimental cryo-EM density maps. CryoRes significantly outperforms all of the state-of-the-art competing resolution estimation methods, achieving an average RMSE of 2.26 Å for local resolution estimation relative to the currently most reliable FSC-based method blocres, yet requiring only the single final map as input. Further, CryoRes is able to generate a molecular mask for each map, with accuracy 12.12% higher than the masks generated by ResMap. CryoRes is ultra-fast, fully automatic, parameter-free, applicable to cryo-EM subtomogram data, and freely available at https://cryores.zhanglab.net.
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34
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Muenks A, Zepeda S, Zhou G, Veesler D, DiMaio F. Automatic and accurate ligand structure determination guided by cryo-electron microscopy maps. Nat Commun 2023; 14:1164. [PMID: 36859493 PMCID: PMC9976687 DOI: 10.1038/s41467-023-36732-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/15/2023] [Indexed: 03/03/2023] Open
Abstract
Advances in cryo-electron microscopy (cryoEM) and deep-learning guided protein structure prediction have expedited structural studies of protein complexes. However, methods for accurately determining ligand conformations are lacking. In this manuscript, we develop EMERALD, a tool for automatically determining ligand structures guided by medium-resolution cryoEM density. We show this method is robust at predicting ligands along with surrounding side chains in maps as low as 4.5 Å local resolution. Combining this with a measure of placement confidence and running on all protein/ligand structures in the EMDB, we show that 57% of ligands replicate the deposited model, 16% confidently find alternate conformations, 22% have ambiguous density where multiple conformations might be present, and 5% are incorrectly placed. For five cases where our approach finds an alternate conformation with high confidence, high-resolution crystal structures validate our placement. EMERALD and the resulting analysis should prove critical in using cryoEM to solve protein-ligand complexes.
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Affiliation(s)
- Andrew Muenks
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Samantha Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Guangfeng Zhou
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.
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35
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Burton-Smith RN, Murata K. Cryo-electron Microscopy of Protein Cages. Methods Mol Biol 2023; 2671:173-210. [PMID: 37308646 DOI: 10.1007/978-1-0716-3222-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein cages are one of the most widely studied objects in the field of cryogenic electron microscopy-encompassing natural and synthetic constructs, from enzymes assisting protein folding such as chaperonin to virus capsids. Tremendous diversity of morphology and function is demonstrated by the structure and role of proteins, some of which are nearly ubiquitous, while others are present in few organisms. Protein cages are often highly symmetrical, which helps improve the resolution obtained by cryo-electron microscopy (cryo-EM). Cryo-EM is the study of vitrified samples using an electron probe to image the subject. A sample is rapidly frozen in a thin layer on a porous grid, attempting to keep the sample as close to a native state as possible. This grid is kept at cryogenic temperatures throughout imaging in an electron microscope. Once image acquisition is complete, a variety of software packages may be employed to carry out analysis and reconstruction of three-dimensional structures from the two-dimensional micrograph images. Cryo-EM can be used on samples that are too large or too heterogeneous to be amenable to other structural biology techniques like NMR or X-ray crystallography. In recent years, advances in both hardware and software have provided significant improvements to the results obtained using cryo-EM, recently demonstrating true atomic resolution from vitrified aqueous samples. Here, we review these advances in cryo-EM, especially in that of protein cages, and introduce several tips for situations we have experienced.
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Affiliation(s)
- Raymond N Burton-Smith
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute for Natural Sciences, Okazaki, Aichi, Japan
- National Institute for Physiological Sciences (NIPS), National Institute for Natural Sciences, Okazaki, Aichi, Japan
| | - Kazuyoshi Murata
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute for Natural Sciences, Okazaki, Aichi, Japan.
- National Institute for Physiological Sciences (NIPS), National Institute for Natural Sciences, Okazaki, Aichi, Japan.
- Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan.
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36
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Li J, Rahmani H, Abbasi Yeganeh F, Rastegarpouyani H, Taylor DW, Wood NB, Previs MJ, Iwamoto H, Taylor KA. Structure of the Flight Muscle Thick Filament from the Bumble Bee, Bombus ignitus, at 6 Å Resolution. Int J Mol Sci 2022; 24:377. [PMID: 36613818 PMCID: PMC9820631 DOI: 10.3390/ijms24010377] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/28/2022] Open
Abstract
Four insect orders have flight muscles that are both asynchronous and indirect; they are asynchronous in that the wingbeat frequency is decoupled from the frequency of nervous stimulation and indirect in that the muscles attach to the thoracic exoskeleton instead of directly to the wing. Flight muscle thick filaments from two orders, Hemiptera and Diptera, have been imaged at a subnanometer resolution, both of which revealed a myosin tail arrangement referred to as “curved molecular crystalline layers”. Here, we report a thick filament structure from the indirect flight muscles of a third insect order, Hymenoptera, the Asian bumble bee Bombus ignitus. The myosin tails are in general agreement with previous determinations from Lethocerus indicus and Drosophila melanogaster. The Skip 2 region has the same unusual structure as found in Lethocerus indicus thick filaments, an α-helix discontinuity is also seen at Skip 4, but the orientation of the Skip 1 region on the surface of the backbone is less angled with respect to the filament axis than in the other two species. The heads are disordered as in Drosophila, but we observe no non-myosin proteins on the backbone surface that might prohibit the ordering of myosin heads onto the thick filament backbone. There are strong structural similarities among the three species in their non-myosin proteins within the backbone that suggest how one previously unassigned density in Lethocerus might be assigned. Overall, the structure conforms to the previously observed pattern of high similarity in the myosin tail arrangement, but differences in the non-myosin proteins.
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Affiliation(s)
- Jiawei Li
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA
| | - Hamidreza Rahmani
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA
| | - Fatemeh Abbasi Yeganeh
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA
| | - Hosna Rastegarpouyani
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA
| | - Dianne W. Taylor
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA
| | - Neil B. Wood
- Department of Molecular Physiology & Biophysics, University of Vermont, Larner College of Medicine, Burlington, VT 05405, USA
| | - Michael J. Previs
- Department of Molecular Physiology & Biophysics, University of Vermont, Larner College of Medicine, Burlington, VT 05405, USA
| | - Hiroyuki Iwamoto
- Scattering and Imaging Division, Japan Synchrotron Radiation Research Institute, SPring-8, Hyogo 679-5198, Japan
| | - Kenneth A. Taylor
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA
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37
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Beton JG, Cragnolini T, Kaleel M, Mulvaney T, Sweeney A, Topf M. Integrating model simulation tools and
cryo‐electron
microscopy. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Joseph George Beton
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Birkbeck and University College London London UK
| | - Manaz Kaleel
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Thomas Mulvaney
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Aaron Sweeney
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Maya Topf
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
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38
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Sorzano COS, Vilas JL, Ramírez-Aportela E, Krieger J, Del Hoyo D, Herreros D, Fernandez-Giménez E, Marchán D, Macías JR, Sánchez I, Del Caño L, Fonseca-Reyna Y, Conesa P, García-Mena A, Burguet J, García Condado J, Méndez García J, Martínez M, Muñoz-Barrutia A, Marabini R, Vargas J, Carazo JM. Image processing tools for the validation of CryoEM maps. Faraday Discuss 2022; 240:210-227. [PMID: 35861059 DOI: 10.1039/d2fd00059h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The number of maps deposited in public databases (Electron Microscopy Data Bank, EMDB) determined by cryo-electron microscopy has quickly grown in recent years. With this rapid growth, it is critical to guarantee their quality. So far, map validation has primarily focused on the agreement between maps and models. From the image processing perspective, the validation has been mostly restricted to using two half-maps and the measurement of their internal consistency. In this article, we suggest that map validation can be taken much further from the point of view of image processing if 2D classes, particles, angles, coordinates, defoci, and micrographs are also provided. We present a progressive validation scheme that qualifies a result validation status from 0 to 5 and offers three optional qualifiers (A, W, and O) that can be added. The simplest validation state is 0, while the most complete would be 5AWO. This scheme has been implemented in a website https://biocomp.cnb.csic.es/EMValidationService/ to which reconstructed maps and their ESI can be uploaded.
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Affiliation(s)
- C O S Sorzano
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - J L Vilas
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | | | - J Krieger
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - D Del Hoyo
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - D Herreros
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | | | - D Marchán
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - J R Macías
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - I Sánchez
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - L Del Caño
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - Y Fonseca-Reyna
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - P Conesa
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - A García-Mena
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - J Burguet
- Depto. de Óptica, Univ. Complutense de Madrid, Pl. Ciencias, 1, 28040, Madrid, Spain
| | - J García Condado
- Biocruces Bizkaia Instituto Investigación Sanitaria, Cruces Plaza, 48903, Barakaldo, Bizkaia, Spain
| | | | - M Martínez
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - A Muñoz-Barrutia
- Univ. Carlos III de Madrid, Avda. de la Universidad 30, 28911, Leganés, Madrid, Spain
| | - R Marabini
- Escuela Politécnica Superior, Univ. Autónoma de Madrid, CSIC, C. Francisco Tomás y Valiente, 11, 28049, Madrid, Spain
| | - J Vargas
- Depto. de Óptica, Univ. Complutense de Madrid, Pl. Ciencias, 1, 28040, Madrid, Spain
| | - J M Carazo
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
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Urzhumtsev A, Lunin VY. Analytic modeling of inhomogeneous-resolution maps in cryo-electron microscopy and crystallography. IUCRJ 2022; 9:728-734. [PMID: 36381145 PMCID: PMC9634607 DOI: 10.1107/s2052252522008260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Refinement of macromolecular atomic models versus experimental maps in crystallography and cryo-electron microscopy is a critical step in structure solution. For an appropriate comparison, model maps should mimic the imperfections in the experimental maps, mainly atomic disorder and limited resolution, which are often inhomogeneous over the molecular region. In the suggested method, these model maps are calculated as the sum of atomic contributions expressed through a specifically designed function describing a solitary spherical wave. Thanks to this function, atomic contributions are analytically expressed through their atomic displacement parameter and local resolution, a value now associated with each atom. Such a full analytic dependence of inhomogeneous-resolution map values on model parameters permits the refinement of all of these parameters together.
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Affiliation(s)
- Alexandre Urzhumtsev
- Centre for Integrative Biology, Institute of Genetics and Molecular and Cellular Biology, Illkirch 67404, France
- Département de Physique, Université de Lorraine, Vandoeuvre-lès-Nancy 54506, France
| | - Vladimir Y. Lunin
- Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino 142290, Russian Federation
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40
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Zhou W, Yadav GP, Yang X, Qin F, Li C, Jiang QX. Cryo-EM structure-based selection of computed ligand poses enables design of MTA-synergic PRMT5 inhibitors of better potency. Commun Biol 2022; 5:1054. [PMID: 36192627 PMCID: PMC9530242 DOI: 10.1038/s42003-022-03991-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 09/13/2022] [Indexed: 12/31/2022] Open
Abstract
Projected potential of 2.5-4.0 Å cryo-EM structures for structure-based drug design is not well realized yet. Here we show that a 3.1 Å structure of PRMT5 is suitable for selecting computed poses of a chemical inhibitor and its analogs for enhanced potency. PRMT5, an oncogenic target for various cancer types, has many inhibitors manifesting little cooperativity with MTA, a co-factor analog accumulated in MTAP-/- cells. To achieve MTA-synergic inhibition, a pharmacophore from virtual screen leads to a specific inhibitor (11-2 F). Cryo-EM structures of 11-2 F / MTA-bound human PRMT5/MEP50 complex and its apo form resolved at 3.1 and 3.2 Å respectively show that 11-2 F in the catalytic pocket shifts the cofactor-binding pocket away by ~2.0 Å, contributing to positive cooperativity. Computational analysis predicts subtype specificity of 11-2 F among PRMTs. Structural analysis of ligands in the binding pockets is performed to compare poses of 11-2 F and its redesigned analogs and identifies three new analogs predicted to have significantly better potency. One of them, after synthesis, is ~4 fold more efficient in inhibiting PRMT5 catalysis than 11-2 F, with strong MTA-synergy. These data suggest the feasibility of employing near-atomic resolution cryo-EM structures and computational analysis of ligand poses for small molecule therapeutics.
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Affiliation(s)
- Wei Zhou
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Gaya P Yadav
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
- Laboratory of Molecular Physiology and Biophysics, Hauptman-Woodward Medical Research Institute, Buffalo, NY, 14203, USA
- G.P.Y at the Department of Biochemistry and Biophysics, Texas A &M University, College Station, TX, 77843, USA
| | - Xiaozhi Yang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Feng Qin
- Department of Physiology and Biophysics, the State University of New York at Buffalo, Buffalo, NY, 14214, USA
| | - Chenglong Li
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA.
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.
- Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA.
| | - Qiu-Xing Jiang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA.
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.
- Laboratory of Molecular Physiology and Biophysics, Hauptman-Woodward Medical Research Institute, Buffalo, NY, 14203, USA.
- Department of Physiology and Biophysics, the State University of New York at Buffalo, Buffalo, NY, 14214, USA.
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41
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Tenjo-Castaño F, Sofos N, López-Méndez B, Stutzke LS, Fuglsang A, Stella S, Montoya G. Structure of the TnsB transposase-DNA complex of type V-K CRISPR-associated transposon. Nat Commun 2022; 13:5792. [PMID: 36184667 PMCID: PMC9527255 DOI: 10.1038/s41467-022-33504-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
CRISPR-associated transposons (CASTs) are mobile genetic elements that co-opted CRISPR-Cas systems for RNA-guided transposition. Here we present the 2.4 Å cryo-EM structure of the Scytonema hofmannii (sh) TnsB transposase from Type V-K CAST, bound to the strand transfer DNA. The strand transfer complex displays an intertwined pseudo-symmetrical architecture. Two protomers involved in strand transfer display a catalytically competent active site composed by DDE residues, while other two, which play a key structural role, show active sites where the catalytic residues are not properly positioned for phosphodiester hydrolysis. Transposon end recognition is accomplished by the NTD1/2 helical domains. A singular in trans association of NTD1 domains of the catalytically competent subunits with the inactive DDE domains reinforces the assembly. Collectively, the structural features suggest that catalysis is coupled to protein-DNA assembly to secure proper DNA integration. DNA binding residue mutants reveal that lack of specificity decreases activity, but it could increase transposition in some cases. Our structure sheds light on the strand transfer reaction of DDE transposases and offers new insights into CAST transposition. The cryo-EM structure of the type VK CRISPR-associated TnsB transposase sheds light onto RNA-guided transposition, providing new possibilities to redesign CRISPR-associated transposon systems.
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Affiliation(s)
- Francisco Tenjo-Castaño
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, 2200, Copenhagen, Denmark
| | - Nicholas Sofos
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, 2200, Copenhagen, Denmark
| | - Blanca López-Méndez
- Protein Purification and Characterisation Facility, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, 2200, Copenhagen, Denmark
| | - Luisa S Stutzke
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, 2200, Copenhagen, Denmark
| | - Anders Fuglsang
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, 2200, Copenhagen, Denmark
| | - Stefano Stella
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, 2200, Copenhagen, Denmark.,Twelve Bio ApS, Ole Maaløes Vej 3, 2200, Copenhagen, Denmark
| | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, 2200, Copenhagen, Denmark.
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42
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Abstract
Cryo-electron microscopy (CryoEM) has become a vital technique in structural biology. It is an interdisciplinary field that takes advantage of advances in biochemistry, physics, and image processing, among other disciplines. Innovations in these three basic pillars have contributed to the boosting of CryoEM in the past decade. This work reviews the main contributions in image processing to the current reconstruction workflow of single particle analysis (SPA) by CryoEM. Our review emphasizes the time evolution of the algorithms across the different steps of the workflow differentiating between two groups of approaches: analytical methods and deep learning algorithms. We present an analysis of the current state of the art. Finally, we discuss the emerging problems and challenges still to be addressed in the evolution of CryoEM image processing methods in SPA.
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Affiliation(s)
- Jose Luis Vilas
- Biocomputing Unit, Centro
Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - Jose Maria Carazo
- Biocomputing Unit, Centro
Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - Carlos Oscar S. Sorzano
- Biocomputing Unit, Centro
Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
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Girbig M, Xie J, Grötsch H, Libri D, Porrua O, Müller CW. Architecture of the yeast Pol III pre-termination complex and pausing mechanism on poly(dT) termination signals. Cell Rep 2022; 40:111316. [PMID: 36070694 DOI: 10.1016/j.celrep.2022.111316] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/01/2022] [Accepted: 08/15/2022] [Indexed: 12/20/2022] Open
Abstract
RNA polymerase (Pol) III is specialized to transcribe short, abundant RNAs, for which it terminates transcription on polythymine (dT) stretches on the non-template (NT) strand. When Pol III reaches the termination signal, it pauses and forms the pre-termination complex (PTC). Here, we report cryoelectron microscopy (cryo-EM) structures of the yeast Pol III PTC and complementary functional states at resolutions of 2.7-3.9 Å. Pol III recognizes the poly(dT) termination signal with subunit C128 that forms a hydrogen-bond network with the NT strand and, thereby, induces pausing. Mutating key interacting residues interferes with transcription termination in vitro, impairs yeast growth, and causes global termination defects in vivo, confirming our structural results. Additional cryo-EM analysis reveals that C53-C37, a Pol III subcomplex and key termination factor, participates indirectly in Pol III termination. We propose a mechanistic model of Pol III transcription termination and rationalize why Pol III, unlike Pol I and Pol II, terminates on poly(dT) signals.
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Affiliation(s)
- Mathias Girbig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Juanjuan Xie
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Helga Grötsch
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Domenico Libri
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Odil Porrua
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany.
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Cryo-electron microscopy and image classification reveal the existence and structure of the coxsackievirus A6 virion. Commun Biol 2022; 5:898. [PMID: 36056184 PMCID: PMC9438360 DOI: 10.1038/s42003-022-03863-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 08/18/2022] [Indexed: 12/18/2022] Open
Abstract
Coxsackievirus A6 (CV-A6) has recently overtaken enterovirus A71 and CV-A16 as the primary causative agent of hand, foot, and mouth disease worldwide. Virions of CV-A6 were not identified in previous structural studies, and it was speculated that the virus is unique among enteroviruses in using altered particles with expanded capsids to infect cells. In contrast, the virions of other enteroviruses are required for infection. Here we used cryo-electron microscopy (cryo-EM) to determine the structures of the CV-A6 virion, altered particle, and empty capsid. We show that the CV-A6 virion has features characteristic of virions of other enteroviruses, including a compact capsid, VP4 attached to the inner capsid surface, and fatty acid-like molecules occupying the hydrophobic pockets in VP1 subunits. Furthermore, we found that in a purified sample of CV-A6, the ratio of infectious units to virions is 1 to 500. Therefore, it is likely that virions of CV-A6 initiate infection, like those of other enteroviruses. Our results provide evidence that future vaccines against CV-A6 should target its virions instead of the antigenically distinct altered particles. Furthermore, the structure of the virion provides the basis for the rational development of capsid-binding inhibitors that block the genome release of CV-A6. A cryo-EM structure for the three conformers of coxsackievirus A6 provides insight into the infection process of this enterovirus, which is responsible for numerous cases of hand, foot, and mouth disease.
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Ramírez-Aportela E, Carazo JM, Sorzano COS. Higher resolution in cryo-EM by the combination of macromolecular prior knowledge and image-processing tools. IUCRJ 2022; 9:632-638. [PMID: 36071808 PMCID: PMC9438491 DOI: 10.1107/s2052252522006959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Single-particle cryo-electron microscopy has become a powerful technique for the 3D structure determination of biological molecules. The last decade has seen an astonishing development of both hardware and software, and an exponential growth of new structures obtained at medium-high resolution. However, the knowledge accumulated in this field over the years has hardly been utilized as feedback in the reconstruction of new structures. In this context, this article explores the use of the deep-learning approach deepEMhancer as a regularizer in the RELION refinement process. deepEMhancer introduces prior information derived from macromolecular structures, and contributes to noise reduction and signal enhancement, as well as a higher degree of isotropy. These features have a direct effect on image alignment and reduction of overfitting during iterative refinement. The advantages of this combination are demonstrated for several membrane proteins, for which it is especially useful because of their high disorder and flexibility.
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Affiliation(s)
- Erney Ramírez-Aportela
- Biocomputing Unit, National Centre for Biotechnology (CNB CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain
| | - Jose M. Carazo
- Biocomputing Unit, National Centre for Biotechnology (CNB CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain
| | - Carlos Oscar S. Sorzano
- Biocomputing Unit, National Centre for Biotechnology (CNB CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain
- Universidad CEU San Pablo, Campus Urb. Montepríncipe, Boadilla del Monte, Madrid 28668, Spain
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46
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Chung JM, Durie CL, Lee J. Artificial Intelligence in Cryo-Electron Microscopy. Life (Basel) 2022; 12:1267. [PMID: 36013446 PMCID: PMC9410485 DOI: 10.3390/life12081267] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Cryo-electron microscopy (cryo-EM) has become an unrivaled tool for determining the structure of macromolecular complexes. The biological function of macromolecular complexes is inextricably tied to the flexibility of these complexes. Single particle cryo-EM can reveal the conformational heterogeneity of a biochemically pure sample, leading to well-founded mechanistic hypotheses about the roles these complexes play in biology. However, the processing of increasingly large, complex datasets using traditional data processing strategies is exceedingly expensive in both user time and computational resources. Current innovations in data processing capitalize on artificial intelligence (AI) to improve the efficiency of data analysis and validation. Here, we review new tools that use AI to automate the data analysis steps of particle picking, 3D map reconstruction, and local resolution determination. We discuss how the application of AI moves the field forward, and what obstacles remain. We also introduce potential future applications of AI to use cryo-EM in understanding protein communities in cells.
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Affiliation(s)
- Jeong Min Chung
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si 14662, Gyeonggi, Korea
| | - Clarissa L. Durie
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Jinseok Lee
- Department of Biomedical Engineering, Kyung Hee University, Yongin-si 17104, Gyeonggi, Korea
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Jiménez de la Morena J, Conesa P, Fonseca YC, de Isidro-Gómez FP, Herreros D, Fernández-Giménez E, Strelak D, Moebel E, Buchholz TO, Jug F, Martinez-Sanchez A, Harastani M, Jonic S, Conesa JJ, Cuervo A, Losana P, Sánchez I, Iceta M, Del Cano L, Gragera M, Melero R, Sharov G, Castaño-Díez D, Koster A, Piccirillo JG, Vilas JL, Otón J, Marabini R, Sorzano COS, Carazo JM. ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation. J Struct Biol 2022; 214:107872. [PMID: 35660516 PMCID: PMC7613607 DOI: 10.1016/j.jsb.2022.107872] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/26/2022] [Accepted: 05/28/2022] [Indexed: 11/25/2022]
Abstract
Image processing in cryogenic electron tomography (cryoET) is currently at a similar state as Single Particle Analysis (SPA) in cryogenic electron microscopy (cryoEM) was a few years ago. Its data processing workflows are far from being well defined and the user experience is still not smooth. Moreover, file formats of different software packages and their associated metadata are not standardized, mainly since different packages are developed by different groups, focusing on different steps of the data processing pipeline. The Scipion framework, originally developed for SPA (de la Rosa-Trevín et al., 2016), has a generic python workflow engine that gives it the versatility to be extended to other fields, as demonstrated for model building (Martínez et al., 2020). In this article, we provide an extension of Scipion based on a set of tomography plugins (referred to as ScipionTomo hereafter), with a similar purpose: to allow users to be focused on the data processing and analysis instead of having to deal with multiple software installation issues and the inconvenience of switching from one to another, converting metadata files, managing possible incompatibilities, scripting (writing a simple program in a language that the computer must convert to machine language each time the program is run), etcetera. Additionally, having all the software available in an integrated platform allows comparing the results of different algorithms trying to solve the same problem. In this way, the commonalities and differences between estimated parameters shed light on which results can be more trusted than others. ScipionTomo is developed by a collaborative multidisciplinary team composed of Scipion team engineers, structural biologists, and in some cases, the developers whose software packages have been integrated. It is open to anyone in the field willing to contribute to this project. The result is a framework extension that combines the acquired knowledge of Scipion developers in close collaboration with third-party developers, and the on-demand design of functionalities requested by beta testers applying this solution to actual biological problems.
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Affiliation(s)
| | - P Conesa
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Y C Fonseca
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | | | - D Herreros
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | | | - D Strelak
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain; Masaryk University, Brno, Czech Republic
| | - E Moebel
- Inria Rennes - Bretagne Atlantique, Rennes
| | - T O Buchholz
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Germany; Center for Systems Biology Dresden (CSBD), Germany
| | - F Jug
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Germany; Fondazione Human Technopole, Milan, Italy
| | - A Martinez-Sanchez
- University of Oviedo, Department of Computer Sciences, Oviedo, Spain; Health Research Institute of Asturias (ISPA), Oviedo, Spain
| | - M Harastani
- IMPMC-UMR 7590 CNRS, Sorbonne Université, MNHN, Paris, France
| | - S Jonic
- IMPMC-UMR 7590 CNRS, Sorbonne Université, MNHN, Paris, France
| | - J J Conesa
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - A Cuervo
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - P Losana
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - I Sánchez
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - M Iceta
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - L Del Cano
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - M Gragera
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - R Melero
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - G Sharov
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - D Castaño-Díez
- BioEM Lab, Biozentrum, University of Basel, Basel, Switzerland
| | - A Koster
- University of Leiden, Ultrastructural and molecular imaging, Leiden, The Netherlands
| | - J G Piccirillo
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - J L Vilas
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - J Otón
- Alba Synchrotron - CELLS (ICTS), Barcelona, Spain
| | - R Marabini
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain; Superior Polytechnic School. Univ. Autónoma of Madrid. Madrid, Spain
| | - C O S Sorzano
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - J M Carazo
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
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Cryo-EM structures show the mechanistic basis of pan-peptidase inhibition by human α 2-macroglobulin. Proc Natl Acad Sci U S A 2022; 119:e2200102119. [PMID: 35500114 PMCID: PMC9181621 DOI: 10.1073/pnas.2200102119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Human α2-macroglobulin (hα2M) is an ∼720-kDa homotetrameric particle with pan-peptidase inhibitory functions that transits between an open native conformation and a closed induced state, in which endopeptidases are trapped upon cleavage of an accessible bait region. We determined the molecular mechanism of this function through eight cryo–electron microscopy (cryo-EM) structures, which revealed that the hα2M subunits are organized in two flexible modules that undergo independent expanded-to-compact transitions. In the induced state, a reactive thioester bond triggers covalent linking of the proteinase, and a receptor-binding domain is exposed on the tetramer surface for binding to its specific cellular receptor for internalization and clearance from circulation. These results elucidate the long-awaited molecular mechanism of a historical suicidal inhibitory trap. Human α2-macroglobulin (hα2M) is a multidomain protein with a plethora of essential functions, including transport of signaling molecules and endopeptidase inhibition in innate immunity. Here, we dissected the molecular mechanism of the inhibitory function of the ∼720-kDa hα2M tetramer through eight cryo–electron microscopy (cryo-EM) structures of complexes from human plasma. In the native complex, the hα2M subunits are organized in two flexible modules in expanded conformation, which enclose a highly porous cavity in which the proteolytic activity of circulating plasma proteins is tested. Cleavage of bait regions exposed inside the cavity triggers rearrangement to a compact conformation, which closes openings and entraps the prey proteinase. After the expanded-to-compact transition, which occurs independently in the four subunits, the reactive thioester bond triggers covalent linking of the proteinase, and the receptor-binding domain is exposed on the tetramer surface for receptor-mediated clearance from circulation. These results depict the molecular mechanism of a unique suicidal inhibitory trap.
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Wang Z, Patwardhan A, Kleywegt GJ. Validation analysis of EMDB entries. Acta Crystallogr D Struct Biol 2022; 78:542-552. [PMID: 35503203 PMCID: PMC9063848 DOI: 10.1107/s205979832200328x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/23/2022] [Indexed: 11/17/2022] Open
Abstract
The Electron Microscopy Data Bank (EMDB) is the central archive of the electron cryo-microscopy (cryo-EM) community for storing and disseminating volume maps and tomograms. With input from the community, EMDB has developed new resources for the validation of cryo-EM structures, focusing on the quality of the volume data alone and that of the fit of any models, themselves archived in the Protein Data Bank (PDB), to the volume data. Based on recommendations from community experts, the validation resources are developed in a three-tiered system. Tier 1 covers an extensive and evolving set of validation metrics, including tried and tested metrics as well as more experimental ones, which are calculated for all EMDB entries and presented in the Validation Analysis (VA) web resource. This system is particularly useful for cryo-EM experts, both to validate individual structures and to assess the utility of new validation metrics. Tier 2 comprises a subset of the validation metrics covered by the VA resource that have been subjected to extensive testing and are considered to be useful for specialists as well as nonspecialists. These metrics are presented on the entry-specific web pages for the entire archive on the EMDB website. As more experience is gained with the metrics included in the VA resource, it is expected that consensus will emerge in the community regarding a subset that is suitable for inclusion in the tier 2 system. Tier 3, finally, consists of the validation reports and servers that are produced by the Worldwide Protein Data Bank (wwPDB) Consortium. Successful metrics from tier 2 will be proposed for inclusion in the wwPDB validation pipeline and reports. The details of the new resource are described, with an emphasis on the tier 1 system. The output of all three tiers is publicly available, either through the EMDB website (tiers 1 and 2) or through the wwPDB ftp sites (tier 3), although the content of all three will evolve over time (fastest for tier 1 and slowest for tier 3). It is our hope that these validation resources will help the cryo-EM community to obtain a better understanding of the quality and of the best ways to assess the quality of cryo-EM structures in EMDB and PDB.
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Affiliation(s)
- Zhe Wang
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Ardan Patwardhan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Gerard J. Kleywegt
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
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50
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DeVore K, Chiu PL. Probing Structural Perturbation of Biomolecules by Extracting Cryo-EM Data Heterogeneity. Biomolecules 2022; 12:628. [PMID: 35625556 PMCID: PMC9138638 DOI: 10.3390/biom12050628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 02/04/2023] Open
Abstract
Single-particle cryogenic electron microscopy (cryo-EM) has become an indispensable tool to probe high-resolution structural detail of biomolecules. It enables direct visualization of the biomolecules and opens a possibility for averaging molecular images to reconstruct a three-dimensional Coulomb potential density map. Newly developed algorithms for data analysis allow for the extraction of structural heterogeneity from a massive and low signal-to-noise-ratio (SNR) cryo-EM dataset, expanding our understanding of multiple conformational states, or further implications in dynamics, of the target biomolecule. This review provides an overview that briefly describes the workflow of single-particle cryo-EM, including imaging and data processing, and new methods developed for analyzing the data heterogeneity to understand the structural variability of biomolecules.
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Affiliation(s)
| | - Po-Lin Chiu
- School of Molecular Sciences, Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA;
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